When student reporters at Mount St. Mary’s University, a small Catholic institution in Maryland, published an article in January that quoted the university’s president likening struggling freshmen to bunnies that should be drowned, they knew it might get a big reaction.

It finally came this week, it appears — in the form of a pink slip for the faculty adviser of the campus newspaper.

The university informed the adviser, Ed Egan, that he had been disloyal and was now fired, a move seen by many on the campus in Emmitsburg as a retaliatory strike.

The decision, along with other recent punishments of faculty members at Mount St. Mary’s, has triggered outrage well beyond its rural campus in northern Maryland, earning condemnation from thousands of academics across the country as well as national monitors of academic and journalistic freedom.

The article, by Rebecca Schisler and Ryan Golden, was published in The Mountain Echo under Mr. Egan’s tutelage on Jan. 19 and presented two explosive pieces of news.

The report said that the administration was planning to cull struggling freshmen from the institution as part of an effort to improve retention numbers — a big factor in rankings published in outlets like U.S. News & World Report — and that the university’s president, Simon Newman, had used disturbing language to sell the idea to a skeptical professor last fall.

“This is hard for you because you think of the students as cuddly bunnies, but you can’t,” Mr. Newman is quoted as saying. “You just have to drown the bunnies.”

He added, “Put a Glock to their heads.”

Mr. Newman declined a request for an interview through a spokesman, but he has apologized for his choice of words and explained that his retention proposal was intended to help students at risk of academic failure and possibly suffocating debt.

Mount St. Mary’s said in a statement that Mr. Egan had been fired for violating the “code of conduct and acceptable use policies.” It declined to provide further details.

But Mr. Egan said in an interview that he had no doubt that the article was the cause of his termination. “There’s no other possible explanation,” he said.

John Coyne, the chairman of the university’s board, said in an interview on Wednesday that while he could not discuss personnel matters, Mr. Egan had manipulated The Echo’s student journalists into portraying the retention program negatively.

“Ed, as the faculty adviser, could really frame the battlefield, if you will, around what the issue was,” Mr. Coyne said. “We had a president in a private conversation with a colleague says the bad-metaphor-hall-of-fame statement, and that was the story. And the position behind it about a retention program that was never enacted, was suddenly lost in the conversation.”

Mr. Egan and both student reporters, who said they had spent weeks investigating their article, rejected Mr. Coyne’s depiction of editorial manipulation. (The private conversation, the students reported, was relayed by two professors who were there.)

“There was no pressure at all,” Ms. Schisler, a junior, said. “We are a student-run paper. All of the articles are the ideas of students, and all of them are written by students.”

Mr. Golden, a senior who is also The Echo’s managing editor, said the newspaper’s staff members had been blindsided by the administration’s move to fire Mr. Egan, who, he said, had been a staunch advocate of their work.

“We were really appalled by it,” Mr. Golden said. “He’s really a good mentor for a lot of students at this school. He absolutely encouraged us to pursue journalistic integrity, absolutely encouraged us to be ethical, to be fair, to be thorough, to be objective and to do the best work that we could.”

Mr. Newman, a former private equity chief executive, was hired last spring to help raise the college’s national profile and increase its endowment. Some faculty members have since pushed back against what they see as his sharp-elbowed business approach.

Mr. Egan’s dismissal was the third case in less than a week of faculty members’ facing censure from Mr. Newman’s administration. The cases were being portrayed by some professors and alumni as a concerted effort to purge the faculty of those with dissenting views.

On the same day that Mr. Egan was fired, Thane Naberhaus, an associate professor of philosophy who has repeatedly criticized Mr. Newman’s policies, was also dismissed. Three days earlier, David Rehm, who had raised concerns about the retention proposal, was stripped of his role as provost.

A petition protesting the firings was circulated among academics on Tuesday by a former philosophy professor at Mount St. Mary’s. It had more than 5,000 signatures by the next day.

The Student Press Law Center, which promotes freedom of the press, said it was alarmed by The Mountain Echo case, and would reach out to its student reporters. The American Association-University Professors, an academic freedom group, wrote a letter to Mr. Newman on Tuesday criticizing the lack of any hearing before the abrupt firing of Mr. Naberhaus, who was tenured.

“Coming, as it did, on the heels of public criticism over statements attributed to you, the dismissal raises the question whether it was in response to this criticism,” Hans-Joerg Tiede, the group’s associate secretary, wrote.

Dismissal letters provided to Mr. Egan and Dr. Naberhaus accused the educators of disloyalty to the university.

“As an employee of Mount St. Mary’s University, you owe a duty of loyalty to this university and to act in a manner consistent with the duty,” read the letter addressed to Dr. Naberhaus and signed by Mr. Newman. “However, your recent actions, in my opinion and that of others, have violated that duty and clearly justify your termination.”

In an interview, Dr. Naberhaus took issue with the absence of detail in the university’s explanation of cause.

“It’s the kind of thing you could expect in a George Orwell novel or something like that,” he said. “But you wouldn’t think this would happen in the real world, or at least not the United States of America.”

Mr. Egan, speaking from his home, said he was exploring his options for recourse. For now, he is forbidden to enter the campus where he has taught law since 2009 — a ban he finds gut-wrenching.

He attended Mount St. Mary’s as a student, as did his father, he said. Mr. Egan later served as an alumni chapter president and as an unpaid assistant coach of the college’s women’s basketball team. He even served for a time as a trustee.

Later, when he was asked to direct Mount St. Mary’s pre-law program, “I considered it the highest honor of my life,” he said.

“I love Mount St. Mary’s and its history and its mission — and until recently, I’ve been excited about its future.”